[quote=@Sho Minazuki]
<Snipped quote by Triple A>

Good and evil are defined by actions, both methods and results, but intentions will always blur that line. This is the simplest form of how to make good and bad characters and some that are near the middle, but if you want to make it even more convoluted... Take a page from Metal Gear Solid. They blur the lines of good and bad so frequently you yourself even find it hard to trust characters you meet. I can't explain how they do it. I only just got into the series' deeper story.

Using character example, I considered putting Lucius, my senior character as an antagonist, even though originally I planned on writing a new one for that. The reason being was that he had the ruthlessness and methodical approach that the cool calm collected types of villains have. I moved him over to the senior side in the end though.
[/quote]

Metal Gear Solid frequently shows that even "villains" have kinder, un-villain like personality traits. Well, when they're not trying to kill everyone who are against their goals. Take a look at Sniper Wolf- Even though she is part of a terrorist organization who hijacked a nuke, she wounded, then used Meryl to draw out snake, basically told snake she would dedicate her life to killing him, turns out to have a soft spot for animals, particularly wolves, and even shows regret for joining said terrorist organization. There are probably more and better examples in MGS, but sniper wolf was always the character I regretted killing. 

I could also say that many of the "good" characters also have traits deem villainy, but an example escapes me at the moment.